Nonpareil protocols

View Nonpareil computational protocol

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Nonpareil specifications

Information


Unique identifier OMICS_01419
Name Nonpareil
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License Artistic License version 2.0
Computer skills Advanced
Version 3.3.1
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Konstantinos Konstantinidis <>

Additional information


An online version is available at http://enve-omics.ce.gatech.edu/nonpareil/submit

Information


Unique identifier OMICS_01419
Name Nonpareil
Interface Web user interface
Restrictions to use None
Input format FASTA,FASTQ
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Konstantinos Konstantinidis <>

Additional information


An online version is available at http://enve-omics.ce.gatech.edu/nonpareil/submit

Publication for Nonpareil

Nonpareil in pipelines

 (4)
2017
PMCID: 5364173
PMID: 28392779
DOI: 10.3389/fmicb.2017.00442

[…] employing sortmerna version 2.0 (). the number of unique sequences per gene was calculated as described previously (). in addition, coverage was determined for the rrna-depleted datasets using nonpareil version 2.4 (). corresponding curves were subsequently generated in r (version 3.2.5; r development core team 2014)., protein extraction was performed either by direct cell lysis […]

2017
PMCID: 5502489
PMID: 28693474
DOI: 10.1186/s12864-017-3918-9

[…] of less than 20 [−min_qual_mean 20], and removed all sequences contains any ambiguous bases (n) [−ns_max_n 0]., after quality filtering, we assessed the level of coverage of each metagenome using nonpareil, a statistical program that uses read redundancy to estimate sequence coverage []., most assemblies were performed on a local server (48 intel® xeon® cpu e5–2680 v3 @ 2.50 ghz processors, […]

2017
PMCID: 5502489
PMID: 28693474
DOI: 10.1186/s12864-017-3918-9

[…] taken to complete assembly were calculated using an in-house bash script., all tables and figures were drawn in r v3.4.0 or microsoft excel. figure was generated using the freely-available tool nonpareil. nonpareil estimates the percentage sequence coverage of metagenomes (as a fraction of 1) using either the forward or reverse sequence reads. these values are then plotted using a scatter […]

2015
PMCID: 4597393
PMID: 26451236
DOI: 10.1186/s40793-015-0069-y

[…] with bowtie2 [] and alignment statistics were recovered with samtools []. the overall alignment rate was 99.9 %. the coverage of the genome was further assessed from the unassembled reads using nonpareil [], which gave an estimated coverage of 100 %, indicating the sequencing effort was more than sufficient to capture all of the genome (4.2 gbp actual effort, compared to 150 mbp estimated […]


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Nonpareil in publications

 (8)
PMCID: 5756336
PMID: 29304850
DOI: 10.1186/s40168-017-0392-1

[…] article, the three samples will be denoted as w2, w9 and w15. sequence coverage was high for all three samples, ranging from 80 to 94% completion (see additional file : table s2) as estimated by nonpareil []. taxonomic classification from unassembled reads using metaphlan2 and metaxa2 yielded improved resolution over the assembled 16s rrna gene sequences (fig. ). the biased estimation […]

PMCID: 5566222
PMID: 28827715
DOI: 10.1038/s41598-017-08783-4

[…] unknown and could belong to novel viral genotypes. also the viral genotype richness was variable among the investigated viromes and this was confirmed by diversity indices calculated by means of the nonpareil program. all viromes were dominated by dsdna viruses mainly belonging to siphoviridae, myoviridae and podoviridae (order caudovirales), although the contribution of single genotypes […]

PMCID: 5502489
PMID: 28693474
DOI: 10.1186/s12864-017-3918-9

[…] of less than 20 [−min_qual_mean 20], and removed all sequences contains any ambiguous bases (n) [−ns_max_n 0]., after quality filtering, we assessed the level of coverage of each metagenome using nonpareil, a statistical program that uses read redundancy to estimate sequence coverage []., most assemblies were performed on a local server (48 intel® xeon® cpu e5–2680 v3 @ 2.50 ghz processors, […]

PMCID: 5430908
PMID: 28432307
DOI: 10.1038/s41598-017-00896-0

[…] was obtained and sequenced by shotgun strategy with illumina technology. quality filtering yielded 12.3 gbp for further analysis. as an initial approach to the data, the reads were analysed with nonpareil, which provided a 92% estimate for the average coverage in socompa, suggesting that assembly and binning might be feasible. idba_ud was used for assembly since it can deal with differential […]

PMCID: 5069759
PMID: 27822527
DOI: 10.1128/mSystems.00003-16

[…] from further analysis. metagenome contigs were assigned to various taxonomic levels by nbc classifier (). average metagenome coverage and sequence diversity were computed for each sample with nonpareil () set at default parameters. ags was computed for each metagenome sample and polynucleobacter bin with microbecensus (). fraggenescan () was also used to predict the protein-coding genes […]


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Nonpareil institution(s)
Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Ford ES&T Building, Atlanta, GA, USA; School of Biology, Georgia Institute of Technology, Ford ES&T Building, Atlanta, GA, USA; School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford ES&T Building, Atlanta, GA, USA
Nonpareil funding source(s)
Supported by U.S. Department of Energy (Award DE-SC0006662) and by U. S. National Science Foundation (Award No 1241046).

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